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Insights into human genetic variation and population history from 929 diverse genomes

Anders Bergström, View ORCID ProfileShane A. McCarthy, Ruoyun Hui, Mohamed A. Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm, Hélène Blanché, Jean-François Deleuze, Howard Cann, Swapan Mallick, David Reich, Manjinder S. Sandhu, Pontus Skoglund, Aylwyn Scally, Yali Xue, Richard Durbin, Chris Tyler-Smith
doi: https://doi.org/10.1101/674986
Anders Bergström
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
2The Francis Crick Institute, London, NW1 1AT, UK
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  • For correspondence: ab34@sanger.ac.uk cts@sanger.ac.uk
Shane A. McCarthy
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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  • ORCID record for Shane A. McCarthy
Ruoyun Hui
3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
4McDonald Institute for Archaeological Research, University of Cambridge, CB2 3ER, UK
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Mohamed A. Almarri
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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Qasim Ayub
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
5Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Malaysia
6School of Science, Monash University Malaysia, 47500 Bandar Sunway, Malaysia
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Petr Danecek
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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Yuan Chen
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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Sabine Felkel
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
7Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
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Pille Hallast
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
8Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
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Jack Kamm
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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Hélène Blanché
9Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
10GENMED Labex, Paris, France, ANR-10-LABX-0013
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Jean-François Deleuze
9Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
10GENMED Labex, Paris, France, ANR-10-LABX-0013
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Howard Cann
9Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, 75010 Paris, France
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Swapan Mallick
11Department of Genetics, Harvard Medical School, Boston, 02115, USA
12Broad Institute of Harvard and MIT, Cambridge, 02142, USA
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David Reich
11Department of Genetics, Harvard Medical School, Boston, 02115, USA
12Broad Institute of Harvard and MIT, Cambridge, 02142, USA
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Manjinder S. Sandhu
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
13Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
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Pontus Skoglund
2The Francis Crick Institute, London, NW1 1AT, UK
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Aylwyn Scally
3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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Yali Xue
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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Richard Durbin
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
3Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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Chris Tyler-Smith
1Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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  • For correspondence: ab34@sanger.ac.uk cts@sanger.ac.uk
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Abstract

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

Footnotes

  • ↵† Deceased.

  • ftp://ngs.sanger.ac.uk/production/hgdp/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 27, 2019.
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Insights into human genetic variation and population history from 929 diverse genomes
Anders Bergström, Shane A. McCarthy, Ruoyun Hui, Mohamed A. Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm, Hélène Blanché, Jean-François Deleuze, Howard Cann, Swapan Mallick, David Reich, Manjinder S. Sandhu, Pontus Skoglund, Aylwyn Scally, Yali Xue, Richard Durbin, Chris Tyler-Smith
bioRxiv 674986; doi: https://doi.org/10.1101/674986
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Insights into human genetic variation and population history from 929 diverse genomes
Anders Bergström, Shane A. McCarthy, Ruoyun Hui, Mohamed A. Almarri, Qasim Ayub, Petr Danecek, Yuan Chen, Sabine Felkel, Pille Hallast, Jack Kamm, Hélène Blanché, Jean-François Deleuze, Howard Cann, Swapan Mallick, David Reich, Manjinder S. Sandhu, Pontus Skoglund, Aylwyn Scally, Yali Xue, Richard Durbin, Chris Tyler-Smith
bioRxiv 674986; doi: https://doi.org/10.1101/674986

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